Structural and functional insights into the recognition of mono- and di-acetyllysine histone tail modifications by the ATAD2 and ATAD2B bromodomains

Epigenomic patterns play important roles in cell type specification marking genomic regulatory elements for the recruitment of a variety of effector proteins. There are many different histone modifications, and among them acetyllysine plays an important role in a number of processes including gene regulation. ATAD2 (ATPase family, AAA+ domain-containing protein 2) and its highly conserved paralog ATAD2B are both bromodomain-containing chromatin reader proteins. ATAD2 has been shown to bind to acetyllysines on the core histone proteins, but the ligand recognition of the ATAD2B bromodomain remains unknown. In addition, the functional relevance and genome-wide acetyllysine pattern recognition by these bromodomain proteins is poorly understood. ATAD2 is overexpressed in multiple types of solid tumors, and its expression is correlated with poor clinical outcomes, including increased risk for metastasis and recurrence in breast cancer. Little is known about the function of ATAD2B, or its role in cancer. Here, we identify and compare the structures and histone ligands of ATAD2 and ATAD2B bromodomains. We show that these bromodomains selectively recognize H4K5acK12ac and H4K5acK8ac di-acetyllysine marks, respectively. Further, we discovered a novel 5’ alternative donor splice site in the exons that encode the ATAD2B bromodomain. This splicing event results in the skipping of 5 critical amino acid residues in the ligand binding pocket. We then show that this ATAD2B isoform lacks the ability to bind to acetyllysines in vitro. Finally, we performed comprehensive epigenomic profiling of the ATAD2/B acetyllysine ligands by ChIP-seq in MCF7 cells. These results reveal unique patterns of histone H4 acetyllysines and demonstrate they are associated with distinctive chromatin states. Ongoing work seeks to define the recruitment of ATAD2/B to these regions, and to understand the functional relevance of histone ligand recognition on breast cancer gene expression programs